None
Clindamycin
Vancomycin
Ciprofloxacin
Ampicillin
Cefaperazone
Metronidazole
Streptomycin
diversity vs colonization
alpha diversity
communities colonized to higher levels have lower diversity (alpha)
association between cfu and alpha (invsimpson and shannon - NS)
cfu vs # of otus (NS)
shared otus?
beta diversity
highly infected communities are most different than untreated
separation between untreated mice and all the highly infected communities (>1e6)
communities that recover/elimnate cdifficile are more diverse
difference in diversity between highly infected
more change w/low diversity?
more change with high cfu?
need to remove dependence of daily sampling?
Alpha Diversity
## [[1]]
## [[1]]
##
## Call:
## lm(formula = get(variable_name) ~ CFU, data = data_frame)
##
## Residuals:
## Min 1Q Median 3Q Max
## -3.331 -3.077 -1.845 1.670 28.555
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.337e+00 9.199e-02 36.277 < 2e-16 ***
## CFU -1.136e-08 1.903e-09 -5.972 2.69e-09 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 4.2 on 2426 degrees of freedom
## (130 observations deleted due to missingness)
## Multiple R-squared: 0.01449, Adjusted R-squared: 0.01408
## F-statistic: 35.66 on 1 and 2426 DF, p-value: 2.693e-09
## [[1]]
## [[1]]
##
## Call:
## lm(formula = get(variable_name) ~ CFU, data = data_frame)
##
## Residuals:
## Min 1Q Median 3Q Max
## -27.83 -25.29 -12.67 21.22 195.27
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.916e+01 6.536e-01 44.616 < 2e-16 ***
## CFU -6.609e-08 1.352e-08 -4.888 1.09e-06 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 29.84 on 2426 degrees of freedom
## (130 observations deleted due to missingness)
## Multiple R-squared: 0.009751, Adjusted R-squared: 0.009343
## F-statistic: 23.89 on 1 and 2426 DF, p-value: 1.087e-06
## [[1]]
## [[1]]
##
## Call:
## lm(formula = get(variable_name) ~ CFU, data = data_frame)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.0640 -1.0409 -0.5456 1.0386 3.3083
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.076e+00 2.473e-02 43.499 < 2e-16 ***
## CFU -2.068e-09 5.116e-10 -4.042 5.46e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.129 on 2426 degrees of freedom
## (130 observations deleted due to missingness)
## Multiple R-squared: 0.00669, Adjusted R-squared: 0.00628
## F-statistic: 16.34 on 1 and 2426 DF, p-value: 5.463e-05
## [[1]]
## [[1]]
##
## Call:
## lm(formula = get(variable_name) ~ CFU, data = data_frame)
##
## Residuals:
## Min 1Q Median 3Q Max
## -2.474 -2.302 -1.224 1.509 29.398
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.481e+00 8.673e-02 28.601 < 2e-16 ***
## CFU -4.698e-09 1.478e-09 -3.178 0.00151 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 3.132 on 1646 degrees of freedom
## (89 observations deleted due to missingness)
## Multiple R-squared: 0.006098, Adjusted R-squared: 0.005494
## F-statistic: 10.1 on 1 and 1646 DF, p-value: 0.001511
## [[1]]
## [[1]]
##
## Call:
## lm(formula = get(variable_name) ~ CFU, data = data_frame)
##
## Residuals:
## Min 1Q Median 3Q Max
## -23.21 -20.92 -12.96 17.59 194.36
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.441e+01 7.030e-01 34.720 <2e-16 ***
## CFU -2.910e-08 1.198e-08 -2.428 0.0153 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 25.39 on 1646 degrees of freedom
## (89 observations deleted due to missingness)
## Multiple R-squared: 0.00357, Adjusted R-squared: 0.002964
## F-statistic: 5.897 on 1 and 1646 DF, p-value: 0.01527
## [[1]]
## [[1]]
##
## Call:
## lm(formula = get(variable_name) ~ CFU, data = data_frame)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.9334 -0.9090 -0.5984 0.9040 3.2837
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 9.469e-01 2.745e-02 34.500 <2e-16 ***
## CFU -1.065e-09 4.678e-10 -2.277 0.0229 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.9912 on 1646 degrees of freedom
## (89 observations deleted due to missingness)
## Multiple R-squared: 0.00314, Adjusted R-squared: 0.002534
## F-statistic: 5.185 on 1 and 1646 DF, p-value: 0.02291
